How can onchocerciasis elimination in Africa be accelerated? Modelling the impact of increased ivermectin treatment frequency and complementary vector control

Background: Great strides have been made toward onchocerciasis elimination by mass drug administration (MDA) of ivermectin. Focusing on MDA-eligible areas, we investigated where the elimination goal can be achieved by 2025 by continuation of current practice (annual MDA with ivermectin) and where intensification or additional vector control is required. We did not consider areas hypoendemic for onchocerciasis with loiasis coendemicity where MDA is contraindicated. Methods: We used 2 previously published mathematical models, ONCHOSIM and EPIONCHO, to simulate future trends in microfilarial prevalence for 80 different settings (defined by precontrol endemicity and past MDA frequency and coverage) under different future treatment scenarios (annual, biannual, or quarterly MDA with different treatment coverage through 2025, with or without vector control strategies), assessing for each strategy whether it eventually leads to elimination. Results: Areas with 40%–50% precontrol microfilarial prevalence and ≥10 years of annual MDA may achieve elimination with a further 7 years of annual MDA, if not achieved already, according to both models. For most areas with 70%–80% precontrol prevalence, ONCHOSIM predicts that either annual or biannual MDA is sufficient to achieve elimination by 2025, whereas EPIONCHO predicts that elimination will not be achieved even with complementary vector control. Conclusions: Whether elimination will be reached by 2025 depends on precontrol endemicity, control history, and strategies chosen from now until 2025. Biannual or quarterly MDA will accelerate progress toward elimination but cannot guarantee it by 2025 in high-endemicity areas. Long-term concomitant MDA and vector control for high-endemicity areas might be useful

Role of a Fur homolog in iron metabolism in Nitrosomonas europaea

<p>Abstract</p> <p>Background</p> <p>In response to environmental iron concentrations, many bacteria coordinately regulate transcription of genes involved in iron acquisition via the ferric uptake regulation (Fur) system. The genome of <it>Nitrosomonas europaea</it>, an ammonia-oxidizing bacterium, carries three genes (NE0616, NE0730 and NE1722) encoding proteins belonging to Fur family.</p> <p>Results</p> <p>Of the three <it>N. europaea fur </it>homologs, only the Fur homolog encoded by gene NE0616 complemented the <it>Escherichia coli </it>H1780 <it>fur </it>mutant. A <it>N. europaea fur:kanP </it>mutant strain was created by insertion of kanamycin-resistance cassette in the promoter region of NE0616 <it>fur </it>homolog. The total cellular iron contents of the <it>fur:kanP </it>mutant strain increased by 1.5-fold compared to wild type when grown in Fe-replete media. Relative to the wild type, the <it>fur:kanP </it>mutant exhibited increased sensitivity to iron at or above 500 μM concentrations. Unlike the wild type, the <it>fur:kanP </it>mutant was capable of utilizing iron-bound ferrioxamine without any lag phase and showed over expression of several outer membrane TonB-dependent receptor proteins irrespective of Fe availability.</p> <p>Conclusions</p> <p>Our studies have clearly indicated a role in Fe regulation by the Fur protein encoded by <it>N. europaea </it>NE0616 gene. Additional studies are required to fully delineate role of this <it>fur </it>homolog.</p

Preoperative chemoradiation with capecitabine, irinotecan and cetuximab in rectal cancer: significance of pre-treatment and post-resection RAS mutations

Background: The influence of EGFR pathway mutations on cetuximab-containing rectal cancer preoperative chemoradiation (CRT) is uncertain. Methods: In a prospective phase II trial (EXCITE), patients with magnetic resonance imaging (MRI)-defined non-metastatic rectal adenocarinoma threatening/involving the surgical resection plane received pelvic radiotherapy with concurrent capecitabine, irinotecan and cetuximab. Resection was recommended 8 weeks later. The primary endpoint was histopathologically clear (R0) resection margin. Pre-planned retrospective DNA pyrosequencing (PS) and next generation sequencing (NGS) of KRAS, NRAS, PIK3CA and BRAF was performed on the pre-treatment biopsy and resected specimen. Results: Eighty-two patients were recruited and 76 underwent surgery, with R0 resection in 67 (82%, 90%CI: 73–88%) (four patients with clinical complete response declined surgery). Twenty–four patients (30%) had an excellent clinical or pathological response (ECPR). Using NGS 24 (46%) of 52 matched biopsies/resections were discrepant: ten patients (19%) gained 13 new resection mutations compared to biopsy (12 KRAS, one PIK3CA) and 18 (35%) lost 22 mutations (15 KRAS, 7 PIK3CA). Tumours only ever testing RAS wild-type had significantly greater ECPR than tumours with either biopsy or resection RAS mutations (14/29 [48%] vs 10/51 [20%], P=0.008), with a trend towards increased overall survival (HR 0.23, 95% CI 0.05–1.03, P=0.055). Conclusions: This regimen was feasible and the primary study endpoint was met. For the first time using pre-operative rectal CRT, emergence of clinically important new resection mutations is described, likely reflecting intratumoural heterogeneity manifesting either as treatment-driven selective clonal expansion or a geographical biopsy sampling miss

Estímulo no crescimento e na hidrólise de ATP em raízes de alface tratadas com humatos de vermicomposto: i - efeito da concentração.

O vermicomposto contém uma concentração elevada de substâncias húmicas e já é bem conhecido o efeito do seu uso sobre as propriedades do solo. No entanto,a ação direta das substâncias húmicas sobre o metabolismo das plantas é menos conhecida. O objetivo deste trabalho foi avaliar o uso de humatos extraídos de vermicomposto de esterco de curral com KOH 0,1 mol L-1 sobre o desenvolvimento e metabolismo de ATP em plântulas de alface. Após a germinação, plântulas de alface foram tratadas com os humatos em concentrações que variaram de 0 a 100 mg L-1 de C, durante quinze dias. Foram avaliados o crescimento da raiz e a atividade das bombas de H+ isoladas da fração microssomal do sistema radicular. Foi observado aumento na matéria fresca e seca do sistema radicular, bem como no número de sítios de mitose, raízes emergidas do eixo principal, na área e no comprimento radiculares, com o uso do humato na concentração de 25 mg L-1 de C. Também foi observado, nessa concentração, aumento significativo na hidrólise de ATP pelas bombas de H+, responsáveis pela geração de energia necessária à absorção de íons e pelo crescimento celular

Molecular coordination of Staphylococcus aureus cell division

The bacterial cell wall is essential for viability, but despite its ability to withstand internal turgor must remain dynamic to permit growth and division. Peptidoglycan is the major cell wall structural polymer, whose synthesis requires multiple interacting components. The human pathogenStaphylococcus aureusis a prolate spheroid that divides in three orthogonal planes. Here, we have integrated cellular morphology during division with molecular level resolution imaging of peptidoglycan synthesis and the components responsible. Synthesis occurs across the developing septal surface in a diffuse pattern, a necessity of the observed septal geometry, that is matched by variegated division component distribution. Synthesis continues after septal annulus completion, where the core division component FtsZ remains. The novel molecular level information requires re-evaluation of the growth and division processes leading to a new conceptual model, whereby the cell cycle is expedited by a set of functionally connected but not regularly distributed components

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Misclassification of malaria as pneumonia in children in sub-Saharan Africa

BackgroundThe World Health Organization (WHO) clinical case definitions for pneumonia were designed to prioritize sensitivity over specificity. In sub-Saharan Africa, the disease that is most likely to be misclassified as pneumonia is Plasmodium falciparum malaria.MethodsBy using chest X-ray positivity as an indicator for pneumonia, we estimated the extent of pneumonia misclassification due to malaria in the Pneumonia Etiology Research for Child Health (PERCH) study. Additionally, we developed a simple model to predict the proportion of pneumonia cases as defined by the WHO that could be attributed to malaria in settings with varying levels of malaria parasitaemia prevalence.ResultsIn the PERCH study, the prevalence of malaria parasitaemia was low (4.7% among WHO pneumonia cases and 1.4% among controls) and we estimate that only 2.5% of WHO pneumonia cases were misclassified. However, when assuming a prevalence of malaria parasitaemia of 24%, corresponding to the average for malaria-endemic areas in Africa, we estimate that 28% of WHO pneumonia cases are misclassified. Among malaria-slide-positive WHO pneumonia cases in PERCH, lower chest wall indrawing [adjusted odds ratio (aOR) =18.1, 95% confidence interval (95% CI): 1.9, 175.8, P = 0.012], crackles on chest auscultation (aOR = 13.1, 95% CI: 1.4, 127.4, P = 0.027), and nasal flaring (aOR = 5.9, 95% CI: 1.1, 32.8, P = 0.041) were associated with chest X-ray positivity.ConclusionIn settings that are typical of sub-Saharan Africa, we predict that one-quarter of WHO-defined pneumonia cases are malaria rather than pneumonia. Among children with WHO pneumonia who also test positive for malaria parasitaemia, clinical features that favour pneumonia include lower chest wall indrawing, nasal flaring, and crackles on chest auscultation

Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly ‘Pseudomonas butanovora’

Soluble butane monooxygenase (sBMO), a three-component di-iron monooxygenase complex expressed by the C2–C9 alkane-utilizing bacterium Thauera butanivorans, was kinetically characterized by measuring substrate specificities for C1–C5 alkanes and product inhibition profiles. sBMO has high sequence homology with soluble methane monooxygenase (sMMO) and shares a similar substrate range, including gaseous and liquid alkanes, aromatics, alkenes and halogenated xenobiotics. Results indicated that butane was the preferred substrate (defined by kcat : Km ratios). Relative rates of oxidation for C1–C5 alkanes differed minimally, implying that substrate specificity is heavily influenced by differences in substrate Km values. The low micromolar Km for linear C2–C5 alkanes and the millimolar Km for methane demonstrate that sBMO is two to three orders of magnitude more specific for physiologically relevant substrates of T. butanivorans. Methanol, the product of methane oxidation and also a substrate itself, was found to have similar Km and kcat values to those of methane. This inability to kinetically discriminate between the C1 alkane and C1 alcohol is observed as a steady-state concentration of methanol during the two-step oxidation of methane to formaldehyde by sBMO. Unlike methanol, alcohols with chain length C2–C5 do not compete effectively with their respective alkane substrates. Results from product inhibition experiments suggest that the geometry of the active site is optimized for linear molecules four to five carbons in length and is influenced by the regulatory protein component B (butane monooxygenase regulatory component; BMOB). The data suggest that alkane oxidation by sBMO is highly specialized for the turnover of C3–C5 alkanes and the release of their respective alcohol products. Additionally, sBMO is particularly efficient at preventing methane oxidation during growth on linear alkanes ≥C2, despite its high sequence homology with sMMO. These results represent, to the best of our knowledge, the first kinetic in vitro characterization of the closest known homologue of sMM

Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA

Liquid biopsy testing utilising Next Generation Sequencing (NGS) is rapidly moving towards clinical adoption for personalised oncology. However, before NGS can fulfil its potential any novel testing approach must identify ways of reducing errors, allowing separation of true low-frequency mutations from procedural artefacts, and be designed to improve upon current technologies. Popular NGS technologies typically utilise two DNA capture approaches; PCR and ligation, which have known limitations and seem to have reached a development plateau with only small, stepwise improvements being made. To maximise the ultimate utility of liquid biopsy testing we have developed a highly versatile approach to NGS: Adaptor Template Oligo Mediated Sequencing (ATOM-Seq). ATOM-Seq's strengths and versatility avoid the major limitations of both PCR- and ligation-based approaches. This technology is ligation free, simple, efficient, flexible, and streamlined, and it offers novel advantages that make it perfectly suited for use on highly challenging clinical material. Using reference and clinical materials, we demonstrate detection of known SNVs down to allele frequencies of 0.1% using as little as 20–25 ng of cfDNA, as well as the ability to detect fusions from RNA. We illustrate ATOM-Seq’s suitability for clinical testing by showing high concordance rates between paired cfDNA and FFPE clinical samples.publishedVersio

Nonattendance in pediatric pulmonary clinics: an ambulatory survey

<p>Abstract</p> <p>Background</p> <p>Nonattendance for scheduled appointments disturbs the effective management of pediatric pulmonary clinics. We hypothesized that the reasons for non-attendance and the necessary solutions might be different in pediatric pulmonary medicine than in other pediatric fields. We therefore investigated the factors associated with nonattendance this field in order to devise a corrective strategy.</p> <p>Methods</p> <p>The effect of age, gender, ethnic origin, waiting time for an appointment and the timing of appointments during the day on nonattendance proportion were assessed. Chi-square tests were used to analyze statistically significant differences of categorical variables. Logistic regression models were used for multivariate analysis.</p> <p>Results</p> <p>A total of 1190 pediatric pulmonology clinic visits in a 21 month period were included in the study. The overall proportion of nonattendance was 30.6%. Nonattendance was 23.8% when there was a short waiting time for an appointment (1–7 days) and 36.3% when there was a long waiting time (8 days and above) (p-value < 0.001). Nonattendance was 28.7% between 8 a.m. to 3 p.m. and 37.5% after 3 p.m. (p = 0.007). Jewish rural patients had 15.4% nonattendance, Jewish urban patients had 31.2% nonattendance and Bedouin patients had 32.9% nonattendance (p < 0.004). Age and gender were not significantly associated with nonattendance proportions. A multivariate logistic regression model demonstrated that the waiting time for an appointment, time of the day, and the patients' origin was significantly associated with nonattendance.</p> <p>Conclusion</p> <p>The factors associated with nonattendance in pediatric pulmonary clinics include the length of waiting time for an appointment, the hour of the appointment within the day and the origin of the patient.</p